Dynamics of disk pairs in a nematic liquid crystal.

We use a hybrid lattice Boltzmann method to study the behavior of sets of ferromagnetic colloidal disks in a nematic liquid crystal. When a weak rotating magnetic field acts on the system, the disks rotate following the magnetic field. This leads to a distortion in the liquid crystal that drives translational motion of the disks.

Dynamics of a disc in a nematic liquid crystal.

We use lattice Boltzmann simulations to study the dynamics of a disc immersed in a nematic liquid crystal. In the absence of external torques, discs with homeotropic anchoring align with their surface normal parallel to the director of the nematic liquid crystal. In the presence of a weak magnetic field a ferromagnetic disc will rotate to equilibrate the elastic torque due to the distortion of the nematic director and the magnetic torque.

Development of personalized tumor biomarkers using massively parallel sequencing.

Clinical management of human cancer is dependent on the accurate monitoring of residual and recurrent tumors. The evaluation of patient-specific translocations in leukemias and lymphomas has revolutionized diagnostics for these diseases. We have developed a method, called personalized analysis of rearranged ends (PARE), which can identify translocations in solid tumors.

Polymorphism discovery in high-throughput resequenced microarray-enriched human genomic loci.

Identifying genetic variants and mutations that underlie human diseases requires development of robust, cost-effective tools for routine resequencing of regions of interest in the human genome. Here, we demonstrate that coupling Applied Biosystems SOLiD system-sequencing platform with microarray capture of targeted regions provides an efficient and robust method for high-coverage resequencing and polymorphism discovery in human protein-coding exons.

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding.

We describe the genome sequencing of an anonymous individual of African origin using a novel ligation-based sequencing assay that enables a unique form of error correction that improves the raw accuracy of the aligned reads to >99.9%, allowing us to accurately call SNPs with as few as two reads per allele. We collected several billion mate-paired reads yielding approximately 18x haploid coverage of aligned sequence and close to 300x clone coverage.

Gene expression-based screening for inhibitors of PDGFR signaling.

Here we describe a proof-of-concept experiment designed to explore the possibility of using gene expression-based high-throughput screening (GE-HTS) to find inhibitors of a signaling cascade, using platelet derived growth factor receptor (PDGFR) signaling as the example. The previously unrecognized ability of aurintricarboxylic acid to inhibit PDGFR signaling, discovered through a screen of 1,739 compounds, demonstrates the feasibility and generalizability of GE-HTS for the discovery of small molecule modulators of any signaling pathway of interest.

A strategy for oligonucleotide microarray probe reduction.

Background: One of the factors limiting the number of genes that can be analyzed on high-density oligonucleotide arrays is that each transcript is probed by multiple oligonucleotide probes. To reduce the number of probes required for each gene, a systematic approach to choosing the most representative probes is needed. A method is presented for reducing the number of probes per gene while maximizing the fidelity to the original array design.